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Description: modify the test python files to use binaries in /usr/bin
Author: Shayan Doust <hello@shayandoust.me>
Last-Update: 2019-09-13
---
--- a/tests/simkaMin/test_simkaMin.py
+++ b/tests/simkaMin/test_simkaMin.py
@@ -16,28 +16,28 @@ NB_CORES = [1, 0]
def create_command(scriptFilename, outputPrefix, k, filter, nb_reads, nb_kmers, nb_cores, input_filename):
outputDir = "k" + str(k) + "_" + filter.replace("-", "") + "_" + str(nb_reads) + "-" + str(nb_kmers) + "_n" + str(nb_cores)
- command = "python " + scriptFilename
+ command = "python3 " + scriptFilename
command += " -in " + input_filename
command += " -out " + outputPrefix + "/" + outputDir
command += " -nb-cores " + str(nb_cores)
command += " -max-memory 100 "
command += " -kmer-size " + str(k)
command += " -nb-kmers " + str(nb_kmers)
- command += " -bin ../../build/bin/simkaMinCore "
+ command += " -bin simkaMinCore "
command += " -max-reads " + str(nb_reads)
command += " " + filter + " "
return command, outputDir
def create_command_update(scriptFilename, outputPrefix, k, filter, nb_reads, nb_kmers, nb_cores, input_filename):
outputDir = "k" + str(k) + "_" + filter.replace("-", "") + "_" + str(nb_reads) + "-" + str(nb_kmers) + "_n" + str(nb_cores)
- command = "python " + scriptFilename
+ command = "python3 " + scriptFilename
command += " -in " + input_filename
command += " -in-to-update " + outputPrefix + "/" + outputDir + "/simkamin"
command += " -nb-cores " + str(nb_cores)
command += " -max-memory 100 "
#command += " -kmer-size " + str(k)
#command += " -nb-kmers " + str(nb_kmers)
- command += " -bin ../../build/bin/simkaMinCore "
+ command += " -bin simkaMinCore "
command += " -max-reads " + str(nb_reads)
command += " " + filter + " "
return command, outputDir
@@ -48,7 +48,7 @@ def create_truth():
for nb_reads in NB_READS:
for nb_kmers in NB_KMERS:
for nb_cores in NB_CORES:
- command, outputDir = create_command("../../simkaMin/simkaMin.py", "truth_simkaMin_symetrical", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
+ command, outputDir = create_command("simkaMin.py", "truth_simkaMin_symetrical", k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
print (command)
ret = os.system(command)
if ret != 0: exit(1)
@@ -146,7 +146,7 @@ def test():
for nb_reads in NB_READS:
for nb_kmers in NB_KMERS:
for nb_cores in NB_CORES:
- command, outputDir = create_command("../../simkaMin/simkaMin.py", dir, k, filter, nb_reads, nb_kmers, nb_cores, " ../../example/simka_input.txt ")
+ command, outputDir = create_command("simkaMin", dir, k, filter, nb_reads, nb_kmers, nb_cores, " ../simka_input.txt ")
print (command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
@@ -166,25 +166,25 @@ def test_append():
os.mkdir(out_dir)
merged_sketch_filename = os.path.join(out_dir, "merged_sketch.bin")
- filename = "../../example/simka_input.txt"
+ filename = "../simka_input.txt"
for line in open(filename):
line = line.strip()
if len(line) == 0: continue
- filename_temp = os.path.join("../../example/test_simkaMin_input_temp.txt")
+ filename_temp = os.path.join("../test_simkaMin_input_temp.txt")
f = open(filename_temp, "w")
f.write(line)
f.close()
sketch_filename = os.path.join(out_dir, "sketch.bin")
- command = "../../build/bin/simkaMinCore sketch -in " + filename_temp + " -out " + sketch_filename + " -nb-kmers 100 -kmer-size 21 -nb-cores 4"
+ command = "simkaMinCore sketch -in " + filename_temp + " -out " + sketch_filename + " -nb-kmers 100 -kmer-size 21 -nb-cores 4"
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
if os.path.exists(merged_sketch_filename):
- command = "../../build/bin/simkaMinCore append -in1 " + merged_sketch_filename + " -in2 " + sketch_filename
+ command = "simkaMinCore append -in1 " + merged_sketch_filename + " -in2 " + sketch_filename
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
@@ -194,12 +194,12 @@ def test_append():
os.remove(filename_temp)
- command = "../../build/bin/simkaMinCore distance -in1 " + merged_sketch_filename + " -in2 " + merged_sketch_filename + " -out " + dir + " -nb-cores 4 "
+ command = "simkaMinCore distance -in1 " + merged_sketch_filename + " -in2 " + merged_sketch_filename + " -out " + dir + " -nb-cores 4 "
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
- command = "../../build/bin/simkaMinCore export -in " + dir + " -in1 " + merged_sketch_filename + " -in2 " + merged_sketch_filename + " -out " + dir
+ command = "simkaMinCore export -in " + dir + " -in1 " + merged_sketch_filename + " -in2 " + merged_sketch_filename + " -out " + dir
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
@@ -223,10 +223,10 @@ def test_matrix_update():
clear(out_dir)
os.mkdir(out_dir)
- filename = "../../example/simka_input.txt"
- filename_temp1 = os.path.join("../../example/test_simkaMin_input_temp1.txt")
+ filename = "../simka_input.txt"
+ filename_temp1 = os.path.join("../test_simkaiMin_input_temp1.txt")
f1 = open(filename_temp1, "w")
- filename_temp2 = os.path.join("../../example/test_simkaMin_input_temp2.txt")
+ filename_temp2 = os.path.join("../test_simkaMin_input_temp2.txt")
f2 = open(filename_temp2, "w")
N=2 #where to split the file
i=0
@@ -241,13 +241,13 @@ def test_matrix_update():
f2.close()
# init
- command, outputDir = create_command("../../simkaMin/simkaMin.py", out_dir, 21, "", 0, 100, 4, filename_temp1)
+ command, outputDir = create_command("simkaMin.py", out_dir, 21, "", 0, 100, 4, filename_temp1)
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
# update
- command, outputDir = create_command_update("../../simkaMin/simkaMin_update.py", out_dir, 21, "", 0, 100, 4, filename_temp2)
+ command, outputDir = create_command_update("simkaMin_update.py", out_dir, 21, "", 0, 100, 4, filename_temp2)
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
--- a/tests/simple_test.py
+++ b/tests/simple_test.py
@@ -91,7 +91,7 @@ def test_parallelization():
#test k=31 t=0
clear()
print("TESTING k=31 t=0")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0"
+command = "simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0"
print(command)
os.system(command + suffix)
test_dists("results_k31_t0")
@@ -99,7 +99,7 @@ test_dists("results_k31_t0")
#test k=21 t=0
clear()
print("TESTING k=21 t=0")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0"
+command = "simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0"
print(command)
os.system(command + suffix)
test_dists("results_k21_t0")
@@ -107,7 +107,7 @@ test_dists("results_k21_t0")
#test k=31 t=2
clear()
print("TESTING k=31 t=2")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0"
+command = "simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0"
print(command)
os.system(command + suffix)
test_dists("results_k31_t2")
@@ -115,7 +115,7 @@ test_dists("results_k31_t2")
#test k=21 t=2
clear()
print("TESTING k=21 t=2")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0"
+command = "simka -in simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0"
print(command)
os.system(command + suffix)
test_dists("results_k21_t2")
@@ -123,9 +123,9 @@ test_dists("results_k21_t2")
#test resources 1
clear()
print("TESTING parallelization")
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000 -verbose 0"
+command = "simka -in simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000 -verbose 0"
os.system(command + suffix)
-command = "../build/bin/simka -in ../example/simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000 -verbose 0"
+command = "simka -in simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000 -verbose 0"
os.system(command + suffix)
test_parallelization()
--- a/example/simple_test.sh
+++ b/example/simple_test.sh
@@ -4,16 +4,7 @@ ADDITIONAL_SIMKA_OPTIONS=$*
# look for simka binary. In devel mode, it's in ../build/bin directory.
# In production mode, it's in ../bin directory.
-if [ -f "../bin/simka" ]
-then
- bindir="../bin"
-elif [ -f "../build/bin/simka" ]
-then
- bindir="../build/bin"
-else
- echo "could not find a compiled simka binary"
- exit 1
-fi
+bindir="/usr/bin"
# run simka
command="$bindir/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output $ADDITIONAL_SIMKA_OPTIONS"
|
